Most of the critics of the movie seem to have gotten a bit caught up with the pedophile vibe that Johnny Depp gives toward Little Red Riding Hood: and with just cause. It wasn't necessary not appropriate for a Disney film. However, I think the scene with the wolf must have distracted people from the movie's greater meaning, which I certainly could understand. Clearly, this was a religious movie as many of Hollywood movies are. There are so many references to the bible. I will mention a few to get you going.
In my opinion, the overall movie is about God and Jesus. The baby was conceived by the witch (who portrays both God (old and new Testament) and the Devil) in an immaculate conception. The baby at the end represents Jesus in the light.
The song "You are not alone" is telling us that Jesus is always with us. It is taken from the Rodgers and Hammerstein song "You'll never walk alone".
The seven sins are portrayed throughout the whole movie with Prince Charming and the Baker's wife exhibiting lust. You can try to pick out the others for yourself. They are all there.
The Baker's father's wife stole from the garden (the Garden of Eden) and basically cast the whole group Into the Woods. The idea of the Woods is the temptation of evil. Bad things happen in the Woods. You are not yourself in the Woods when the Devil whispers in your ear to follow him. In the end, you hear the Baker's wife say bring the child so he can bask in the glow of God.
I think you get the idea. If you watch it again, there are so many references. I won't spell them all out for you as certain inferences can be made differently, like what the giant represents A modern day David and Goliath battle was clearly depicted in the final scene. The Giant, however, has a bigger meaning. I'll let others draw their own conclusions as to what they think she means, and a lot of the other symbolic messages that they threw out there.
When they say you have to choose a side, they are referring to either good or evil. Someone will always be on your side, no matter what choice you make. You have to decide whether or not it will be God or the Devil.
The final third of the movie was the final culmination of the fight of good against evil and what prevails. It was a fairy tale telling the story of the Bible. I'm an agnostic but was still moved by this movie, even if the wolf scene creeped me out too!